I have an 06 soft top with the half doors. I live in CT and see all kinds of weather and temp changes, I haven't had any condensation issues on the inside except on rainy days when I'm all wet and get in the Jeep. But as for overnight condensation, I'd recommend letting the inside air out, try running your heater with the A/C switched on. The A/C will dry out the air a little and help get that moisture out of there.
As for down sides to soft tops my only problem is the scratches that show up on the plastic windows, I'm gonna try a plastic conditioner that pilots use on their plexi windows on planes this spring to see if that works. But the ability to drop the top whenever I want far outweighs any complaints I have about it.
2006 SE 6 Speed, Solar Yellow. Zone 2" Hydro BB, Sway Links, and Steering Stabilizer. 31x10.5-15 Bridgestone Dueler AT Revo. Alpine CDA9813, Polk MM6, Polk C400.4